PsychENCODE’s marker gene selection might be imperfect since some “marker” genes are shared by different cell types. However, it has enough discriminatory power. Using this initial dictionary of marker genes, we can start analyzing 10x data, which consist of these three files:
## %%MatrixMarket matrix coordinate integer general
## 17926 70634 119696200
## 56 1 1
## 139 1 1
## 270 1 1
## 324 1 1
## 375 1 1
## 389 1 1
## 420 1 1
## 557 1 1
## AAACGGGAGATCCCGC.1
## AAATGCCTCCAATGGT.1
## AACCATGTCAGTGCAT.1
## AACCATGTCTGTACGA.1
## AACCGCGTCCGCATAA.1
## AACGTTGGTTCAGGCC.1
## AACTGGTGTACCGGCT.1
## AAGACCTAGTTAACGA.1
## AAGGAGCAGCAATCTC.1
## AAGGAGCTCTGCTGCT.1
## FO538757.2
## SAMD11
## NOC2L
## KLHL17
## PLEKHN1
## PERM1
## HES4
## ISG15
## AGRN
## RNF223
## Joining, by = "ct"
## quartz_off_screen
## 2
## Warning: Removed 4702 rows containing non-finite values (stat_smooth).
## Warning: Removed 4702 rows containing non-finite values (stat_cor).
## Warning: Removed 4702 rows containing missing values (geom_point).